From: Having a BLAST with bioinformatics (and avoiding BLASTphemy)
Parameter | Use | Parameter type | Default setting |
---|---|---|---|
(a) Parameters mentioned in the text and Box 2 | |||
   -M | Matrix | String | BLOSUM62 |
   -r | Reward for a nucleotide match (BLASTNonly) | Integer | 1 |
   -q | Penalty for a nucleotide mismatch (BLASTNonly) | Integer | -3 |
   -G | Cost to open a gap (zero invokes default behavior) | Integer | 0 |
   -E | Cost to extend a gap (zero invokes default behavior) | Integer | 0 |
   -F | Filter query sequence | String | T |
   -W | Word size; default length is used if set to zero | Integer | 0 |
   -z | Effective length of the database (use zero to get the real size) | Real | 0 |
   -e | Expectation value (E) | Real | 10.0 |
(b) Additional useful parameters | |||
   -i | Name of the query file | Filename | "stdin" |
   -m | Alignment viewing options, which include: |  |  |
 |    0 Pairwise alignment |  |  |
 |    1 Query-anchored showing identities |  |  |
 |    2 Query-anchored, no identities |  |  |
 |    7 XML output | Integer | 0 |
   -o | Name of the BLAST report output file | Filename | "stdout" |
   -f | Threshold for extending hits; default is used if set to zero | Integer | 0 |
   -g | Perform gapped alignment (not available with TBLASTX) | T/F | T |
   -Y | Effective length of the search space (use zero get the real size) | Real | 0 |
   -S | Query strands to search against the database (for BLAST [NX], and TBLASTX) 3 is both, 1 is top, 2 is bottom | Integer | 3 |
   -T | Produce HTML output | T/F | F |
   -y | Drop-off (X) for BLAST extensions, in bits (0.0 invokes default behavior) | Real | 0.0 |
   -Z | X drop-off value for final gapped alignment (in bits) | Integer | 0 |